Sunday, September 14, 2014

When I Pointed Out the De Novo Gene Evidence an Evolutionist Came Unglued

Primitive Thinking

It is interesting that evolutionists, who believe they came from primitive apes, display a certain primitive thought in their communications. The latest example is an evolutionist who criticized a book skeptical of evolution. The book made the point that fundamentally new genes are unlikely to have evolved by the usual random change and natural selection mechanisms. The book elaborated on this problem at length. But the evolutionist retorted that this was all wrong:

[The book] claims that the origin of new genes is a mystery, when in fact it is basically a solved problem (as long as you aren’t talking about the origin of the very first genes at the origin of life—and allegedly this book is supposed to be about the Cambrian Explosion, not the origin of life).

In other words, aside from the origin of life, the origin of fundamentally new genes is not a mystery and is basically has been solved by evolutionists.

Look up jingwei and sdic and the literature on their origin. Look up Long et al. 2003. Why can’t you even get these totally obvious basic points right?

The problem is jingwei and Sdic are not fundamentally new genes, but rather have significant similarities to parts of other genes. And the paper he cited did little to resolve this question of how fundamentally new genes arose. In fact, about the only thing the paper did say about the evolution of such genes is that it is rare. That view has since been discarded as too many of these fundamentally new genes have been discovered.

So the evolutionist cited two irrelevant genes and a paper that gave an outdated view, and accused me of missing “totally obvious basic points.”

When I pointed all this out, the evolutionist tried to walk back his points. He claimed that I was the one who brought up fundamentally new genes, and that he merely was referring to genes that are mostly rearrangements of other genes. “Shame!” he vindictively concluded.

And there we have it. At this point the evolutionist is in checkmate. For he has just forfeited his claim that the book is all wrong, that the evolution of new genes is a solved problem, and by extension that evolution is a fact. He cannot now say, “Oh, but I was also referring to fundamentally new genes also.”

He has made it clear that the book’s criticism is on solid ground. For as I pointed out (here and here), the evolutionary reasoning that such genes evolved by the usual random mutations and selection is circular. And the explanations for how this could have happened is little more than hand waving. Even evolutionists agreed it was impossible until, that is, the existence of such genes could not be denied. At that point evolutionists had to come up with some sort of explanation. The result is a speculative idea that relies on serendipity and ignores known, enormous problems.

A theory cannot fail to explain a plethora of fundamental observations and be a fact. Not a scientific fact, at least.

So will the evolutionist admit to any of these things? Will he agree that evolution is not a fact? Of course not. I’ll take the shame and the blame, and all the harsh criticism, if we can just agree on the overwhelming scientific evidence which checkmates evolution. Evolution is not a fact, and it never was.

"The problem is jingwei and Sdic are not fundamentally new genes, but rather have significant similarities to parts of other genes."

The vast majority of genes have this feature. This includes the crucial developmental genes in the bilaterian phyla, most of which are shared across phyla. E.g. hox genes. So I guess you are agreeing that most genes could evolve naturally. Therefore I was right to say the origin of new genes is a solved problem.

Neither Meyer nor you nor anyone else has explained what "fundamentally" new genes are -- these are just weasel words to avoid addressing the evidence for evolution. It's the same game that creationists always play with "kinds", transitional fossils, etc. -- creationists sweep the evidence under the rug by inventing a poorly-defined category and then saying, "oh, evidence X is just within-the-kind evolution, what we demand is X+Y, and we won't tell you what Y is". Shame! And you guys wonder why you get nothing but scorn from scientists. Word games to dismiss evidence will never do anything except reassure the gullible creationist faithful.

Wrong again. As Light, Basile and Elofsson write in their 2014 review which I referenced, “It has even been proposed that the creation of novel genes, a continuous process where most de novo genes are short-lived, is as frequent as gene duplications.” Likewise Neme and Tautz explain, “there is now rapidly increasing evidence that de novo evolution of transcripts and genes is not only a theoretical possibility, but might even have been a rather active process throughout evolution.”

You can’t sweep the evidence under the rug Nick. And blaming me isn’t going to help. In both the origin of life (OOL) problem, and in the origin of new genes during evolutionary history, de novo genes are significant.

So I guess you are agreeing that most genes could evolve naturally. Therefore I was right to say the origin of new genes is a solved problem.

I already answered this question. I specifically addressed both jingwei (gene fusion) and sdic (fission), in response to your earlier comment. The evidence suggests that jingwei and sdic arose from parts lying around. Now whether that can be explained as merely a result of evolution’s random change plus selection is another question. Evolutionists have simply taken this for granted. That approach fell flat on its face in the case of neo Darwinism and adaptation.

Neither Meyer nor you nor anyone else has explained what "fundamentally" new genes are -- these are just weasel words to avoid addressing the evidence for evolution. It's the same game that creationists always play with "kinds", transitional fossils, etc.

Actually these are not weasel words. Evolutionists try to blur the lines but, I’m sorry, zero BLAST hits is an objective measure.

Shame!

Well let’s get back to my question. I think you already answered it, in so many words, but to be sure, you are agreeing that the evolution of de novo genes via the usual random variation plus selection is not a solved problem, right?

"I already answered this question. I specifically addressed both jingwei (gene fusion) and sdic (fission), in response to your earlier comment. The evidence suggests that jingwei and sdic arose from parts lying around. Now whether that can be explained as merely a result of evolution’s random change plus selection is another question. Evolutionists have simply taken this for granted. That approach fell flat on its face in the case of neo Darwinism and adaptation."

Huh? The processes that need to be invoked to explain sdic and jingwei are mutational processes that are known to occur, and natural selection and drift which are known to occur. There aren't even any creationists making any claims for nonfunctional intermediates for these genes. Half the creationists at least seem to accept that they are the product of natural processes -- except Joe here, who apparently doesn't think anything about history can ever be inferred from genomes, even if known, observed mutational processes produce genomic pattern X and we observe pattern X in a genome. Perhaps he's a proponent of the Answers in Genesis "Were you there?" school.

"Well let’s get back to my question. I think you already answered it, in so many words, but to be sure, you are agreeing that the evolution of de novo genes via the usual random variation plus selection is not a solved problem, right?"

Nope. There are a number of studies showing ORFans that are homologous to noncoding DNA in related species, demonstrating that spontaneous-mutation-creating-start-codons is the main thing going on. Also note that standard creationist calculations about the origin of genes, which assume things like a 300-amino acid protein (900 DNA bases) resulting in a soluble protein do not apply to typical ORFans, which, even if they are functional (usually there is no evidence for this, but sometimes there is) are typically short and may not even be producing a functional protein, instead perhaps having regulational or interference "functions".

Huh? The processes that need to be invoked to explain sdic and jingwei are mutational processes that are known to occur, and natural selection and drift which are known to occur.

I don’t disagree, and that may well be the end of the story. The question is not one of mechanism but rather of likelihood and serendipity. For instance, your mechanism argument was also used by neo Darwinists for adaptation and how mere extrapolation of adaptive change accounts for macro evolution. Sure, we had the mechanisms in hand. But there were probability questions and now even evolutionists agree that that story isn’t working. Back to sdic and jingwei. The mutational processes plus selection might be entirely reasonable, but we’re talking about (i) random mutation plus selection finding the initial protein-coding genes, a process that studies have shown to be low probability and (ii) those genes undergoing duplications, fusions, etc., to form new genes which then undergo further mutations to find new functionalities. From what we know of the difficulty in finding protein-coding genes in the rugged hyper-dimensional fitness space, it is not immediately clear that such a process is all there is to it. So genes that somehow evolved and converged to a particular peak in the fitness landscape just so happen to provide the raw materials for a different function in the fitness landscape. Reasonable? Perhaps, I don’t know. These are not easy questions, and it seems to me that it would be scientifically irresponsible to claim we have pretty much figured all this out and that evolution explains it all.

Nope. There are a number of studies showing ORFans that are homologous to noncoding DNA in related species, demonstrating that spontaneous-mutation-creating-start-codons is the main thing going on.

But of course we weren’t talking about those. We were talking about “fundamentally new” genes. I specifically asked you about “de novo” genes. So, again, everything you have said indicates you agree that in that case, the evolutionary explanation is not a solved problem, right?

Also note that standard creationist calculations about the origin of genes, which assume things like a 300-amino acid protein (900 DNA bases) resulting in a soluble protein do not apply to typical ORFans, which, even if they are functional (usually there is no evidence for this, but sometimes there is) are typically short and may not even be producing a functional protein, instead perhaps having regulational or interference "functions".

Yes, agreed, but again, that is not what we’re talking about. Yes, there are plenty of transcribed segments that are of unknown function and may well have no function. We’re not talking about those. We’re talking about de novo genes that are not short snippets and have known, and in many cases, essential functions. Even evolutionists are now admitting that these young genes surprisingly are found to have important and essential functions. See, for example:

"'Nope. There are a number of studies showing ORFans that are homologous to noncoding DNA in related species, demonstrating that spontaneous-mutation-creating-start-codons is the main thing going on.'

But of course we weren’t talking about those. We were talking about “fundamentally new” genes. I specifically asked you about “de novo” genes. So, again, everything you have said indicates you agree that in that case, the evolutionary explanation is not a solved problem, right?"

But these would show up without BLAST hits in standard BLAST searches, since typically one is searching against a database of genes/ORFs, e.g. GENBANK.

If one had a situation where a bunch of closely related species had been sequenced, and one had a long, functional, protein-coding gene and the others didn't have the gene or any homologous non-coding DNA corresponding to it, and an analysis of sequence change rates indicated that it was very improbable that sequence similarity would have been lost between such close relatives, and you had sufficient relatives to make it improbable that they all experienced an independent deletion of that region -- then sure, that would be a mystery. But I have yet to see such a case, and none of the new-genes literature we've been discussing has been about such cases.

The trail will almost always go cold if you go deep enough in any phylogeny, of course, just because sequence change will eventually obliterate any similarity -- particularly for non-coding relatives. But that's a different thing than what you are describing.

It's incredible, really. You've been making an argument about what turns out to be a possibly-non-existent subset of a subset of a subset of new genes -- yet you've been citing articles that are about these larger subsets, where evolutionary explanations are readily available and productive and well-published. This sort of definitional shifting plagues creationist arguments from top to bottom.

No, the Chen paper includes de novo genes. In fact, not only does it include de novo genes, it finds no statistically significant difference in the rate of essentiality. Quote:

“In general, the proportion of new genes that are essential do not differ significantly among the three types of origination mechanisms [i.e., DNA-based duplication, RNA-based duplication and de novo origination]”.

Indeed, the second paper (Reinhardt, et. al.) actually found a higher rate of essentiality for the de novo genes. Quote:

“De novo genes are protein-coding genes with no clear homology to previously existing protein-coding genes. Since their discovery in Drosophila and other species including humans, their existence has been controversial, with some doubt as to how they would arise, whether they produce proteins, and whether they could possibly perform any useful function. Here, we show that RNAi of several Drosophila de novo genes causes lethality – in fact, a higher proportion of de novo genes cause lethality than was found in a similar screen of other young and novel genes.”

No, I’m not shifting definitions. Quote:

“By definition, a recently de novo created gene should not have any homologs at all and even after some time there should not exist any homologs outside closely related species. Rephrased: when searching a database of all genes, the de novo created genes should only have hits in closely related species. Such genes are referred to as orphan genes.” (Light, Basile, Elofsson, “Orphans and new gene origination, a structural and evolutionary perspective”)

The bottom line is this. There are all kinds of ways de novo genes may arise. The question is, how likely are they under RM+NS evolution? The mechanism/process that has been proposed, which calls for a (i) gene birth from non genic sequence, (ii) some genetic engineering experiments, (iii) gene death, cycle (Neme, Tautz, “Evolution: Dynamics of De Novo Gene Emergence”) seems unlikely under RM+NS evolution. The serendipity of RM+NS evolution just happening to produce such an elaborate system is extreme (there is no selective advantage to this system until it actually produces some useful proteins, which is a long way down the road), and the probability of an essential protein rapidly emerging from it are, I think, serious problems. But in any case, to say that this is basically a solved problem is just irresponsible. This new, speculative, model has only recently been proposed.

Cornelius G. Hunter is a graduate of the University of Illinois where
he earned a Ph.D. in Biophysics and Computational Biology. He is
Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot
(Baker/Brazos Press). Dr. Hunter's interest in the theory of evolution
involves the historical and theological, as well as scientific, aspects
of the theory. His website is http://www.darwins-god.blogspot.com/